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<H3>4. Tools within Pizza.py 
</H3>
<P><A HREF = "Section_basics.html#3_4">Th previous section</A> describes how Pizza.py
tools are used in Pizza.py.
</P>
<P>Help on the syntax for invoking a tool and using its methods and
settings can be accessed interactively within Pizza.py itself by
typing "? tool" or "?? tool".  Typing "??" gives a one-line
description of each tool.
</P>
<P>These are the different categories of Pizza.py tools:
</P>
<DIV ALIGN=center><TABLE  BORDER=1 >
<TR><TD >LAMMPS in/out files</TD><TD > chain, data, dump, log, patch, bdump, ldump, tdump</TD></TR>
<TR><TD >ChemCell in/out files</TD><TD > cdata, olog, dump</TD></TR>
<TR><TD >SPPARKS in/out files</TD><TD > olog, dump</TD></TR>
<TR><TD >SPARTA in/out files</TD><TD > sdata, olog, dump</TD></TR>
<TR><TD >Visualization</TD><TD > gl, rasmol, raster, svg, vmd</TD></TR>
<TR><TD >File conversion</TD><TD > cfg, ensight, pdbfile, vtk, xyz</TD></TR>
<TR><TD >GUI wrappers</TD><TD > animate, image, plotview, vcr</TD></TR>
<TR><TD >Plotting</TD><TD > gnu, matlab</TD></TR>
<TR><TD >Miscellaneous</TD><TD > histo, mdump, pair, vec 
</TD></TR></TABLE></DIV>

<P>Within the plotting and viz categories, individual tools share many
common methods, so the tools can often be used interchangeably.  For
example, the same script can produce an animation using either
Raster3d or SVG to generate the movie frames, by simply changing the
line that creates the visualizer object, or by passing the object into
the script as an argument.
</P>
<P>This is the complete list of tools in Pizza.py; the link is to each
tool's documentation page.
</P>
<DIV ALIGN=center><TABLE  BORDER=1 >
<TR><TD ><A HREF = "animate.html">animate.py</A></TD><TD > Animate a series of image files</TD></TR>
<TR><TD ><A HREF = "bdump.html">bdump.py</A></TD><TD > Read LAMMPS dump local files with bond info</TD></TR>
<TR><TD ><A HREF = "data.html">cdata.py</A></TD><TD > Read, write, manipulate <A HREF = "http://www.cs.sandia.gov/~sjplimp/cell.html">Chemcell</A> data files</TD></TR>
<TR><TD ><A HREF = "chain.html">chain.py</A></TD><TD > Create bead-spring chains for LAMMPS input</TD></TR>
<TR><TD ><A HREF = "cfg.html">cfg.py</A></TD><TD > Convert LAMMPS snapshots to CFG format</TD></TR>
<TR><TD ><A HREF = "data.html">data.py</A></TD><TD > Read, write, manipulate LAMMPS data files</TD></TR>
<TR><TD ><A HREF = "dump.html">dump.py</A></TD><TD > Read, write, manipulate dump files and particle attributes</TD></TR>
<TR><TD ><A HREF = "ensight.html">ensight.py</A></TD><TD > Convert LAMMPS snapshots to <A HREF = "http://www.ensight.com">Ensight</A> format</TD></TR>
<TR><TD ><A HREF = "gl.html">gl.py</A></TD><TD > 3d interactive visualization via OpenGL</TD></TR>
<TR><TD ><A HREF = "gnu.html">gnu.py</A></TD><TD > Create plots via <A HREF = "http://www.gnuplot.info">GnuPlot</A> plotting program</TD></TR>
<TR><TD ><A HREF = "histo.html">histo.py</A></TD><TD > Particle density histogram from a dump</TD></TR>
<TR><TD ><A HREF = "image.html">image.py</A></TD><TD > View and manipulate images</TD></TR>
<TR><TD ><A HREF = "ldump.html">ldump.py</A></TD><TD > Read LAMMPS dump files with line info</TD></TR>
<TR><TD ><A HREF = "log.html">log.py</A></TD><TD > Read LAMMPS log files and extract thermodynamic data</TD></TR>
<TR><TD ><A HREF = "matlab.html">matlab.py</A></TD><TD > Create plots via <A HREF = "http://www.mathworks.com">MatLab</A> numerical analysis program</TD></TR>
<TR><TD ><A HREF = "mdump.html">mdump.py</A></TD><TD > Read, write, manipulate mesh dump files</TD></TR>
<TR><TD ><A HREF = "olog.html">olog.py</A></TD><TD > Read other log files (ChemCell, SPPARKS, SPARTA) and extract time-series data</TD></TR>
<TR><TD ><A HREF = "pair.html">pair.py</A></TD><TD > Compute LAMMPS pairwise energies</TD></TR>
<TR><TD ><A HREF = "patch.html">patch.py</A></TD><TD > Create patchy Lennard-Jones particles for LAMMPS input</TD></TR>
<TR><TD ><A HREF = "pdbfile.html">pdbfile.py</A></TD><TD > Read, write PDB files in combo with LAMMPS snapshots</TD></TR>
<TR><TD ><A HREF = "plotview.html">plotview.py</A></TD><TD > Plot multiple vectors from a data set</TD></TR>
<TR><TD ><A HREF = "rasmol.html">rasmol.py</A></TD><TD > 3d visualization via <A HREF = "http://www.openrasmol.org">RasMol</A> program</TD></TR>
<TR><TD ><A HREF = "raster.html">raster.py</A></TD><TD > 3d visualization via <A HREF = "http://www.bmsc.washington.edu/raster3d/raster3d.html">Raster3d</A> program</TD></TR>
<TR><TD ><A HREF = "sdata.html">sdata.py</A></TD><TD > Read, write, manipulate <A HREF = "sparta">SPARTA</A> surface files</TD></TR>
<TR><TD ><A HREF = "svg.html">svg.py</A></TD><TD > 3d visualization via <A HREF = "http://www.w3.org/Graphics/SVG">SVG</A> files</TD></TR>
<TR><TD ><A HREF = "tdump.html">tdump.py</A></TD><TD > Read LAMMPS dump files with triangle info</TD></TR>
<TR><TD ><A HREF = "vcr.html">vcr.py</A></TD><TD > VCR-style GUI for 3d interactive OpenGL visualization</TD></TR>
<TR><TD ><A HREF = "vec.html">vec.py</A></TD><TD > Create numeric vectors from columns in file or list of vecs</TD></TR>
<TR><TD ><A HREF = "vtk.html">vtk.py</A></TD><TD > Convert LAMMPS snapshots to VTK format</TD></TR>
<TR><TD ><A HREF = "vmd.html">vmd.py</A></TD><TD > Wrapper on <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD visualization package</A></TD></TR>
<TR><TD ><A HREF = "xyz.html">xyz.py</A></TD><TD > Convert LAMMPS snapshots to XYZ format 
</TD></TR></TABLE></DIV>

















<P>This diagram represents the different ways tools can be interconnected
by Pizza.py.  Tools within the same red box are tools that are
(roughly) interchangeable.
</P>
<CENTER><IMG SRC = "tools.jpg">
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